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Yorodumi- PDB-6mpq: 1.95 Ang crystal structure of OXA-24/40 beta-lactamase in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mpq | ||||||
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Title | 1.95 Ang crystal structure of OXA-24/40 beta-lactamase in complex the inhibitor ETX2514 | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE/HYDROLASE Inhibitor / beta-lactamase / inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex | ||||||
Function / homology | Function and homology information penicillin binding / cell wall organization / beta-lactamase activity / beta-lactamase Similarity search - Function | ||||||
Biological species | Acinetobacter baumannii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | van den Akker, F. / Kumar, V. | ||||||
Funding support | United States, 1items
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Citation | Journal: MBio / Year: 2019 Title: Targeting Multidrug-ResistantAcinetobacterspp.: Sulbactam and the Diazabicyclooctenone beta-Lactamase Inhibitor ETX2514 as a Novel Therapeutic Agent. Authors: Barnes, M.D. / Kumar, V. / Bethel, C.R. / Moussa, S.H. / O'Donnell, J. / Rutter, J.D. / Good, C.E. / Hujer, K.M. / Hujer, A.M. / Marshall, S.H. / Kreiswirth, B.N. / Richter, S.S. / Rather, P. ...Authors: Barnes, M.D. / Kumar, V. / Bethel, C.R. / Moussa, S.H. / O'Donnell, J. / Rutter, J.D. / Good, C.E. / Hujer, K.M. / Hujer, A.M. / Marshall, S.H. / Kreiswirth, B.N. / Richter, S.S. / Rather, P.N. / Jacobs, M.R. / Papp-Wallace, K.M. / van den Akker, F. / Bonomo, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mpq.cif.gz | 69.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mpq.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 6mpq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mpq_validation.pdf.gz | 805.2 KB | Display | wwPDB validaton report |
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Full document | 6mpq_full_validation.pdf.gz | 805.8 KB | Display | |
Data in XML | 6mpq_validation.xml.gz | 13 KB | Display | |
Data in CIF | 6mpq_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mp/6mpq ftp://data.pdbj.org/pub/pdb/validation_reports/mp/6mpq | HTTPS FTP |
-Related structure data
Related structure data | 3mbzS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 27733.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) Gene: blaOXA-33, bla-OXA-40, blaOXA-24, blaOXA-40, oxa-24, oxa40 Production host: Escherichia coli (E. coli) / References: UniProt: Q8RLA6 |
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#2: Chemical | ChemComp-JXG / ( |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.12 Å3/Da / Density % sol: 70.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: of 0.1 M HEPES sodium salt pH 7.5, 10% (v/v) isopropanol and 20% (w/v) PEG 4000. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→72.52 Å / Num. obs: 34248 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.043 / Rrim(I) all: 0.114 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.791 / Num. unique obs: 2350 / CC1/2: 0.767 / Rpim(I) all: 0.337 / Rrim(I) all: 0.863 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3mbz Resolution: 1.95→37.5 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.079 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.108 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.79 Å2 / Biso mean: 32.085 Å2 / Biso min: 17.79 Å2
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Refinement step | Cycle: final / Resolution: 1.95→37.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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